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Yorodumi- PDB-2erb: AgamOBP1, and odorant binding protein from Anopheles gambiae comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2erb | ||||||
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Title | AgamOBP1, and odorant binding protein from Anopheles gambiae complexed with PEG | ||||||
Components | odorant binding proteinOdorant-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / helix / disulfides | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Anopheles gambiae (African malaria mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Wogulis, M. / Morgan, T. / Ishida, Y. / Leal, W.S. / Wilson, D.K. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2006 Title: The crystal structure of an odorant binding protein from Anopheles gambiae: Evidence for a common ligand release mechanism. Authors: Wogulis, M. / Morgan, T. / Ishida, Y. / Leal, W.S. / Wilson, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2erb.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2erb.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 2erb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/2erb ftp://data.pdbj.org/pub/pdb/validation_reports/er/2erb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is likely a monomer. |
-Components
#1: Protein | Mass: 14547.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anopheles gambiae (African malaria mosquito) Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8I8T0 #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-PEU / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 32% PEG 8000, 250 mM MgCl2, 50 mM Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 8, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88557 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 39215 / Num. obs: 39190 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Monomer of model generated from MAD experiments. Resolution: 1.5→30.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 121865.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.145 Å2 / ksol: 0.380672 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→30.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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